Forensic STR analysis using massive parallel sequencing
Forensic STR analysis using massive parallel sequencing
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DOI：
10.1016/j.fsigen.2012.03.004
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发表时间：
2012-12-01
影响因子：
3.1
通讯作者：
Deforce, Dieter
中科院分区：
文献类型：
--
作者：
Van Neste, Christophe;Van Nieuwerburgh, Filip;Deforce, Dieter
我们探讨了第二代测序（SGS）对多重法医STR扩增子测序的适用性，无论是在单一贡献者样本中，还是在不同比例的多人混合物中。我们比较了商用STR分析试剂盒(Applied Biosystems AmpFlSTR （R) Profiler Plus (R)）的结果，用毛细管电泳和罗氏GS FLX测序进行了分析。提供了一个易于使用的开源软件管道，将从GS FLX FASTA文件开始分析所需的不同步骤链接在一起，从而生成一个FASTA文件，其中包含数据中存在的调用和量化的等位基因。使用罗氏GS FLX钛技术对多路STR扩增子进行测序在技术上是可行的，但该技术并不理想。全长reads比例小，均聚物测序错误率高。该管道将均聚物压缩为单一碱基，以避免这些均聚物引起的错误结果。SGS STR分析管道的定性和定量结果与电泳方法相当。此外，SGS方法提供了额外的信息，并且能够根据数据库中的STR序列调用等位基因亚型。在混合样本中，所有等位基因都来自对混合物贡献至少10%的个体。2012爱思唯尔爱尔兰有限公司版权所有。
We explore the applicability of second generation sequencing (SGS) to sequence multiplexed forensic STR amplicons, both in a single contributor sample as in multiple-person mixtures with different ratios. We compare the results of a commercial STR profiling kit (Applied Biosystems AmpFlSTR (R) Profiler Plus (R)), analyzed both with capillary electrophoresis and with Roche GS FLX sequencing. An easy to use open-source software pipeline is provided, chaining together the different steps needed to start the analysis from a GS FLX FASTA file, resulting in a FASTA file containing the called and quantified alleles present in the data. Sequencing of multiplexed STR amplicons using Roche GS FLX titanium technology is technically feasible but the technology is not ideal for this purpose. The fraction of full length reads is small and the homopolymer sequencing error rate is high. The pipeline compresses the homopolymers to a single base to avoid false results caused by these homopolymers. The qualitative and quantitative results from the SGS STR analysis pipeline are comparable to the electrophoresis method. Additionally, the SGS method provides extra information and is able to call allele subtypes based on STR sequences in a database. In mixed samples, all alleles were reported from individuals that contributed at least 10% to the mixture. (C) 2012 Elsevier Ireland Ltd. All rights reserved.